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add _pkgdown.yml and .github/workflows/pr_check.yml GHA
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‎.github/workflows/pr_check.yml‎

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name: PR CMD check & build site
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on:
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pull_request:
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push:
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paths:
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- 'DESCRIPTION'
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- '**.yml'
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branches:
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- devel
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- RELEASE_3_21
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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CRAN: https://p3m.dev/cran/__linux__/noble/latest
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BIOC_RELEASE: RELEASE_3_21
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jobs:
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set-matrix:
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runs-on: ubuntu-24.04
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outputs:
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matrix: ${{ steps.set.outputs.matrix }}
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dockerfile_exists: ${{ steps.dockerfile.outputs.exists }}
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steps:
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- name: Set Matrix Bioconductor Version
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id: set
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run: |
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MATRIX="{\"include\":[{\"bioc_version\":\"$GITHUB_REF_NAME\"}]}"
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echo "matrix=$MATRIX" >> $GITHUB_OUTPUT
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- name: Check for Dockerfile
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id: dockerfile
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run: |
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echo "exists=$( [ -f ./inst/docker/pkg/Dockerfile ] && echo true || echo false )" >> $GITHUB_OUTPUT
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check:
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needs: set-matrix
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runs-on: ubuntu-latest
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strategy:
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matrix: ${{ fromJson(needs.set-matrix.outputs.matrix) }}
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container: bioconductor/bioconductor_docker:${{ matrix.bioc_version }}
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steps:
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- name: Checkout Repository
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uses: actions/checkout@v4
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with:
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ref: ${{ matrix.bioc_version }}
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- name: Query dependencies
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run: |
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BiocManager::install(c("covr", "BiocCheck"))
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v4
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with:
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path: /usr/local/lib/R/site-library
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key: ${{ runner.os }}-r-${{ matrix.bioc_version }}-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.bioc_version }}-
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- name: Install GPG
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if: ${{ github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }}
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run: sudo apt-get update && sudo apt-get install -y gpg
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- name: Install Dependencies
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run: |
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remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
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BiocManager::install(c("rcmdcheck", "BiocCheck"), ask = FALSE, update = TRUE)
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shell: Rscript {0}
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- name: Check Package
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check")
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shell: Rscript {0}
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- name: Test coverage
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if: ${{ success() && github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }}
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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type = "all",
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install_path = file.path(
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normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"),
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"package"
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)
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)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- name: Upload test results to Codecov
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if: ${{ success() && github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }}
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uses: codecov/codecov-action@v4
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with:
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fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Run BiocCheck
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id: bioccheck
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run: |
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BiocCheck::BiocCheck(
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dir('check', 'tar.gz$', full.names = TRUE),
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`quit-with-status` = TRUE, `no-check-bioc-help` = TRUE
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)
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shell: Rscript {0}
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- name: Build pkgdown
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if: ${{ github.ref == format('refs/heads/{0}', env.BIOC_RELEASE) && github.event_name != 'pull_request' }}
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run: |
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PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()'
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- name: Upload pkgdown artifact
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if: github.ref == format('refs/heads/{0}', env.BIOC_RELEASE)
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uses: actions/upload-pages-artifact@v3
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with:
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path: docs
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dock:
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needs:
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- check
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- set-matrix
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runs-on: ubuntu-24.04
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if: ${{ github.ref == 'refs/heads/devel' && needs.set-matrix.outputs.dockerfile_exists == 'true' }}
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steps:
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- name: Checkout Repository
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if: ${{ success() && github.event_name != 'pull_request' }}
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uses: actions/checkout@v4
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- name: Register repo name
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if: ${{ github.event_name != 'pull_request' }}
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id: reg_repo_name
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run: |
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echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
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- name: Login to Docker Hub
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if: ${{ github.event_name != 'pull_request' }}
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Build and Push Docker
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if: ${{ success() && github.event_name != 'pull_request' }}
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uses: docker/build-push-action@v6
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with:
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context: .
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file: ./inst/docker/pkg/Dockerfile
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push: true
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tags: >
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${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
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${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
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deploy:
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needs: check
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permissions:
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contents: write
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pages: write
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id-token: write
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runs-on: ubuntu-24.04
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steps:
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- name: Deploy to GitHub Pages
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if: ${{ github.ref == format('refs/heads/{0}', env.BIOC_RELEASE) && github.event_name != 'pull_request' }}
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id: deployment
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uses: actions/deploy-pages@v4
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‎_pkgdown.yml‎

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title: SingleCellMultiModal
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url: https://waldronlab.github.io/SingleCellMultiModal
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template:
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bootstrap: 5
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params:
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bootswatch: flatly

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